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FOR IMMEDIATE RELEASE
SUMMARY: Annual concluding symposium for Vassar’s Undergraduate Research Summer Institute to include keynote address by Cal-Berkeley computer scientist Christos Papadimitriou, on September 25
POUGHKEEPSIE, NY – Each summer over 100 combined Vassar students and professors participate in the Undergraduate Research Summer Institute (URSI), an intensive 10-week campus program in which students conduct original scientific research under faculty direction. Together through URSI they create and nurture a tightly knit community of scientific scholars. Each fall at the annual URSI symposium students make presentations about their summer research projects and an invited distinguished scientist provides a keynote address.
The 2013 URSI symposium will be held on Wednesday, September 25, from 3:00-6:45pm in the Villard Room of Main Building, beginning with oral presentations by five of this summer’s student researchers. At 4:15 computer scientist Christos H. Papadimitriou will present his keynote “Computational Insights and the Theory of Evolution”, immediately followed by a gallery of student poster presentations on the all of the 2013 URSI projects (held in areas adjacent to the Villard Room). All activities are free and open to the public.
URSI was founded in 1986 and is among the nation's oldest undergraduate scientific research programs. Complete information on the September 25 symposium and the overall URSI program can be found online at http://ursi.vassar.edu
In his address Papadimitriou will discuss how recent computational techniques have provided unique insights into the theory of evolution. For example, developments such as genetic algorithms, Boolean functions, and unsupervised learning have advanced the understanding certain aspects of evolution and population genetics.
Papadimitriou’s special interest is the theory of algorithms and complexity, and its applications to databases, optimization, Artificial Intelligence, the Internet, game theory, and evolution. His scholarly books includeElements of the Theory of Computation (1982), Combinatorial Optimization: Algorithms and Complexity (1982),The Theory of Database Concurrency Control (1988), Computational Complexity (1994), and Algorithms (2006).
Papadimitriou is the C. Lester Hogan Professor of Electrical Engineering and Computer Science at Cal-Berkeley, where he has taught since 1996. A member of the National Academy of Sciences, the American Academy of Arts and Sciences, and the National Academy of Engineering, his honors also include the Goedel Prize, the Knuth Prize, and several honorary doctorates. In addition to his scholarly articles and books, he has published the novels Turing (2003) and Independence (2012), as well as the graphic novel Logicomix (2010).Papadimitriou earlier taught at Harvard, MIT, Athens Polytechnic, Stanford, and the University of California-San Diego. He graduated from Athens Polytechnic and received his PhD. from Princeton.
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Vassar is located at 124 Raymond Avenue in Poughkeepsie, NY, and directions to the campus can be found athttp:www.vassar.edu/directions. Vassar College is a highly selective, coeducational, independent, residential, liberal arts college founded in 1861.
Tuesday, September 17, 2013
Rockefeller Hall 300
One of the most useful programming languages is TEX, constructed by Donald Knuth, and developed by Leslie Lamport into LATEX, the standard for mathematical typesetting over the last 25 years. If you want to be able to typeset your mathematical work, or even to typeset any of your assignments, LATEX can be very valuable.
I will give a lecture/demonstration of elementary aspects of the LATEX programming language. If you have installed a version of TEX on your laptop, bring it along. On the MAC, install TEXshop. On machines running Microsoft operating systems, install MikTEX. Both of these versions of TEX are freely available on the Web.
May 14th, 2012
1:30pm - 4:00pm
Each student will have 30 minutes to present including time for questions.
1:30 - 2:00 Alexa Dorsey
2:00 - 2:30 Dimitri Wijesinghe - Checkpointing MCMCTree
PAML (Phylogenetic Analysis with Maximum Likelihood) is a bioinformatics software package that includes MCMCTree. MCMCTree performs Bayesian inference (using Markov Chain Monte Carlo methods) on phylogenetic trees and fossil data to calculate when each species in the evolutionary tree originated. One limitation of MCMCTree is that it cannot handle today's large datasets without causing a system crash or taking several months to compute. To address this problem, we implemented a system of checkpointing for MCMCTree. With this system, MCMCtree can begin a calculation and save data as it goes along. If the system is interrupted or crashes, calculations can be restored from the last checkpoint instead of starting from scratch. This infinitely increases the range of data the system can process. This work required conducting computational experiments and comparing the results of checkpointed and non-checkpointed versions of MCMCTree. This presentation will discuss the challenges of experimental reproducibility when working with randomized tools like MCMCTree. With this system in place, biologists will be able to compute datasets such as the evolutionary tree of all mammals and estimate the origin time of all mammalian species based on existing fossil data.
2:30 - 3:00 Mark Adamo - TreeHouse: Tools for Visualizing and Analyzing Datasets from Large-Scale Phylogenetic Inference
Large-scale phylogenetic inference may return sets of thousands of trees, each possibly containing hundreds of taxa. TreeHouse is a phylogenetic tree-querying program that operates on large, highly-compressed sets of trees. I have extended TreeHouse to support multiple modes of visualization and have incorporated support for biological classification data, enabling entirely new hypothesis testing analyses. New filtering operations allow for trees as well as tree sets to be edited, allowing tree data to be tailored to specialized areas of biological inquiry. Memory optimizations make TreeHouse's memory performance scale much better as the size of trees and trees sets increases. In total, the process of implementing these features has also enhanced TreeHouse's viability as a platform for further development of phylogenetic computations. The most recent of these developments is an implementation of the Ancestral Distance Test for correlated trait evolution.
3:00 - 3:30 Tavish Pegram
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